Hi There DnA,
I must say I'm not really sure that I understand what exactly the problem here is but:
Presumably your first problem was that you had a very large track in your GPS (i.e. with many points). And when you downloaded this from your unit into MapSource you could see all the points correctly? (If not it could be that you have not downloaded all the points correctly from the unit, let me know if this is the case)
You should then be able to see the tracks you've downloaded on the 'Tracks' tab on the left handside of the MapSource pane. There may be one track here or multiple tracks, depending on how the tracks were put together. All the points from all of your tracks should be visible if you select all the tracks from the tracks tab (ctrl+a) then right mouse click and select 'show selected tracks on map'
See Below:
It seems to me unlikely that any of the data would be lost in the save itself unless the file has become corrupted, so it seems more likely (to me at this stage) that some part of your track simply wasn't saved correctly.
Looking at this as an example, what's different to yours?
David